An episode of the soap, due to air next week (beg07Jun10), shows character Lucas Johnson, played by Don Gilet, visiting a red light district and attacking a sex worker named Jade.
But several scenes are now being reshot by TV executives as a mark of respect to the families of three murdered prostitutes in Bradford, England.
PhD student Stephen Griffiths, 40, has been charged with the killings.
A representative for the BBC show says, "EastEnders storylines are written many months in advance and any similarity to real-life events is coincidental.
"However, on this occasion, to ensure we do not cause distress to the families involved in the recent tragic events in Bradford we have decided to reshoot some parts of the storyline involving Lucas Johnson."
The news comes shortly after TV bosses in charge of another British soap opera, Coronation Street, cancelled the broadcast of an episode featuring an armed siege after a gunman went on the rampage in North-West England on Wednesday (02Jun10) killing 12 people and injuring another 25 before turning the gun on himself.